Edgar Gabriel MPI derived datatypes Edgar Gabriel

Derived Datatypes Basic idea: interface to describe memory layout of user data structures e.g. a structure in C typedef struct { chara; intb; doublec; } mystruct; Memory layout

Edgar Gabriel Derived Datatype examples E.g. describing a column or a row of a matrix Memory layout in C Memory layout in Fortran

Edgar Gabriel How to describe non- contiguous data structures typedef struct { chara; intb; doublec; } mystruct; using a list-I/O interface, e.g. or baseaddraddress1 address2 gap1 gap2

Edgar Gabriel …or in MPI terminology… a list of sequences …leading to the following interface… MPI_Type_struct (int count, int blocklength[], MPI_Aint displacements[], MPI_Datatype datatypes[], MPI_Datatype *newtype ); MPI_Type_create_struct (int count, int blocklength[], MPI_Aint displacements[], MPI_Datatype datatypes[], MPI_Datatype *newtype );

Edgar Gabriel MPI_Type_struct/MPI_Type_ create_struct MPI_Aint: –Is an MPI Address integer –An integer being able to store a memory address Displacements are considered to be relative offsets  displacement[0] = 0 in most cases!  Displacements are not required to be positive, distinct or in increasing order How to determine the address of an element MPI_Address (void *element, MPI_Aint *address); MPI_Get_address (void *element, MPI_Aint *address);

Edgar Gabriel Addresses in MPI Why not use the & operator in C ? –ANSI C does NOT require that the value of the pointer returned by & is the absolute address of the object! –Might lead to problems in segmented memory space –Usually not a problem In Fortran: all data elements passed to a single MPI_Type_struct call have to be in the same common - block

Edgar Gabriel Type map vs. Type signature Type signature is the sequence of basic datatypes used in a derived datatype, e.g. typesig(mystruct) = {char, int, double} Type map is sequence of basic datatypes + sequence of displacements typemap(mystruct) = {(char,0),(int,8),(double,16)} Type matching rule of MPI: type signature of sender and receiver has to match –Including the count argument in Send and Recv operation (e.g. unroll the description) –Receiver must not define overlapping datatypes –The message need not fill the whole receive buffer

Edgar Gabriel Committing and freeing a datatype If you want to use a datatype for communication or in an MPI-I/O operation, you have to commit it first MPI_Type_commit (MPI_Datatype *datatype); Need not commit a datatype, if just used to create more complex derived datatypes MPI_Type_free (MPI_Datatype *datatype); It is illegal to free any predefined datatypes

Edgar Gabriel Our previous example looks like follows: mystruct mydata; MPI_Address ( &mydata, &baseaddr); MPI_Address ( &mydata.b, &addr1); MPI_Address ( &mydata.c, &addr2); displ[0] = 0; displ[1] = addr1 – baseaddr; displ[2] = addr2 – baseaddr; dtype[0] = MPI_CHAR;blength[0] = 1; dtype[1] = MPI_INT;blength[1] = 1; dtype[2] = MPI_DOUBLE;blength[2] = 1; MPI_Type_struct ( 3, blength, displ, dtype, &newtype ); MPI_Type_commit ( &newtype ); baseaddraddress1 address2

Edgar Gabriel Basically we are done… With MPI_Type_struct we can describe any pattern in the memory Why other MPI datatype constructors ? –Because description of some datatypes can become rather complex –For convenience

Edgar Gabriel MPI_Type_contiguous MPI_Type_contiguous ( int count, MPI_Datatype datatype, MPI_Datatype *newtype ); count elements of the same datatype forming a contiguous chunk in the memory int myvec[4]; MPI_Type_contiguous ( 4, MPI_INT, &mybrandnewdatatype); MPI_Type_commit ( &mybrandnewdatatype ); MPI_Send ( myvec, 1, mybrandnewdatatype, … ); Input datatype can be a derived datatype –End of one element of the derived datatype has to be exactly at the beginning of the next element of the derived datatype

Edgar Gabriel MPI_Type_vector MPI_Type_vector( int count, int blocklength, int stride, MPI_Datatype datatype, MPI_Datatype *newtype ); count blocks of blocklength elements of the same datatype Between the start of each block there are stride elements of the same datatype blocklength =2 stride =3 count =3

Edgar Gabriel Example using MPI_Type_vector Describe a column of a 2-D matrix in C dtype = MPI_DOUBLE; stride = 8; blength = 1; count = 8; MPI_Type_vector (count,blength,stride,dtype,&newtype); MPI_Type_commit (&newtype); Which column you are really sending depends on the pointer which you pass to the according MPI_Send routine!

Edgar Gabriel MPI_Type_hvector MPI_Type_hvector( int count, int blocklength, MPI_Aint stride, MPI_Datatype datatype, MPI_Datatype *newtype ); MPI_Type_create_hvector( int count, int blocklength, MPI_Aint stride, MPI_Datatype datatype, MPI_Datatype *newtype ); Identical to MPI_Type_vector, except that the stride is given in bytes rather than in number of elements

Edgar Gabriel MPI_Type_indexed MPI_Type_indexed( int count, int blocklengths[], int displacements[], MPI_Datatype datatype, MPI_Datatype *newtype ); The number of elements per block do not have to be identical displacements gives the distance from the ‘base’ to the beginning of the block in multiples of the used datatype count = 3blocklengths[0] = 2displacements[0] = 0 blocklengths[1] = 1displacements[1] = 3 blocklengths[2] = 4 displacements[2] = 5

Edgar Gabriel MPI_Type_hindexed MPI_Type_hindexed( int count, int blocklengths[], MPI_Aint displacements[], MPI_Datatype datatype, MPI_Datatype *newtype ); MPI_Type_create_hindexed( int count, int blocklengths[], MPI_Aint displacements[], MPI_Datatype datatype, MPI_Datatype *newtype ); Identical to MPI_Type_indexed, except that the displacements are given in bytes and not in multiples of the datatypes

Edgar Gabriel Duplicating a datatype MPI_Type_dup(MPI_Datatype datatype,MPI_Datatype *newtype); Mainly useful for library developers, e.g. datatype ownership The new datatype has the same ‘committed’ state as the previous datatype –If datatype has already been committed, newtype is committed as well

Edgar Gabriel MPI_Type_create_subarray MPI_Type_create_subarray (int ndims, int sizes[], int subsizes[], int starts[], int order, MPI_Datatype datatype,MPI_Datatype *newtype); Define sub-matrices of n-dimensional data sizes[] : dimension of the entire matrix subsizes[] : dimensions of the submatrix described by the derived data type starts[]: array describing the beginning of the submatrices Order: MPI_ORDER_C for row-major order or MPI_ORDER_FORTRAN for column-major data

Edgar Gabriel Example ndims =2 sizes[0] = 8; sizes[1] = 8; subsizes[0]= 4; subsizes[1] = 2 starts[0] = 2; starts[1] = 4; MPI_Type_create_subarray ( ndims, sizes, subsizes, starts, MPI_ORDER_C, MPI_DOUBLE, &newtype); Dimension 0 Dimension 1

Edgar Gabriel More datatype constructors MPI_Type_create_darray(int size, int rank, int ndims, int gsizes[], int distribs[], int dargs[], int psizes[], int order, MPI_Datatype datatype, MPI_Datatype *newtype); Describe HPF-like data distributions MPI_Type_create_indexed_block( int count, int blocklength, int displs[], MPI_Datatype datatype, MPI_Datatype *newtype ); Further simplification of MPI_Type_indexed

Edgar Gabriel Portable vs. non-portable datatypes Any data type constructors using byte-offsets are considered non-portable –Might rely on data alignment rules given on various platforms Non-portable datatype constructors: –MPI_Type_struct –MPI_Type_hvector/MPI_Type_create_hvector –MPI_Type_hindexed/MPI_Type_create_hindexed Non-portable datatypes are not allowed to be used in –one-sided operations –parallel File I/O operations

Edgar Gabriel A problem with the specification up to now typedef struct { chara; intb; doublec; float d; } mystruct; mystruct mydata[5]; …but just want to send b and c of the structure, however multiple elements of mystruct

Edgar Gabriel …simple description… MPI_Address ( &(mydata[0], &baseaddr); MPI_Address ( &(mydata[0].b, &addr1); MPI_Address ( &(mydata[0].c, &addr2); displ[0] = addr1 - baseaddr; displ[1] = addr2 – baseaddr; dtype[0] = MPI_INT;blength[0] = 1; dtype[1] = MPI_DOUBLE;blength[1] = 1; MPI_Type_struct ( 2, blength, displ, dtype, &newtype ); MPI_Type_commit ( &newtype );

Edgar Gabriel If we use this datatype…. it is ok if we send one element MPI_Send ( mydata, 1, newtype,…); If we send more elements, all data at the receiver will be wrong, except for the first element MPI_Send ( mydata, 5, newtype, …); Memory layout What we send is What we wanted to do is

Edgar Gabriel …so what we missed … …was to tell MPI where the next element of the structure starts –or in other words: we did not tell MPI where the begin and the end of the structure is Two ‘marker’ datatypes introduced in MPI –MPI_LB: lower bound of a structure –MPI_UB: upper bound of a structure

Edgar Gabriel Correct description of the structure would be MPI_Address ( &(mydata[0]), &baseaddr); MPI_Address ( &(mydata[0].b), &addr1); MPI_Address ( &(mydata[0].c), &addr2); MPI_Address ( &(mydata[1]), &addr3); displ[0] = 0; displ[1] = addr1 - baseaddr; displ[2] = addr2 – baseaddr; displ[3] = addr3 – baseaddr; dtype[0] = MPI_LB;blength[0] = 1; dtype[1] = MPI_INT;blength[1] = 1; dtype[2] = MPI_DOUBLE; blength[2] = 1; dtype[3] = MPI_UB;blength[3] = 1; MPI_Type_struct ( 4, blength, displ, dtype, &newtype );

Edgar Gabriel Determining upper- and lower bound Two functions to extract the upper and the lower bound of a datatype MPI_Type_ub ( MPI_Datatype dat, MPI_Aint *ub ); MPI_Type_lb ( MPI_Datatype dat, MPI_Aint *lb );

Edgar Gabriel extent vs. size of a datatype MPI_Type_extent ( MPI_Datatype dat, MPI_Aint *ext); MPI_Type_size ( MPI_Datatype dat, int *size ); extent := upper bound – lower bound; size = amount of bytes really transferred extent size

Edgar Gabriel The MPI-2 view of the same problem (I) Problem with the way MPI-1 treats this problem: upper and lower bound can become messy, if you have derived datatype consisting of derived dataype consisting of derived datatype consisting of… and each of them has MPI_UB and MPI_LB set No way to erase upper and lower bound markers once they are set MPI-2 solution: reset the extent of the datatype MPI_Type_create_resized ( MPI_Datatype datatype, MPI_Aint lb, MPI_Aint extent, MPI_Datatype *newtype ); –Erases all previous lb und ub markers

Edgar Gabriel MPI-2 view of the same problem (II) MPI_Type_get_true_extent ( MPI_Datatype dat, MPI_Aint *lb, MPI_Aint *extent ); The true extent –Extent of the datatype ignoring UB and LB markers: all gaps in the middle are still considered, gaps at the beginning and at the end are removed –E.g. required for intermediate buffering extent true extent

Edgar Gabriel Decoding MPI datatypes An important question for library developers: –Given a datatype handle, can I determine how it was created –Given a datatype handle, can I determine what memory layout it describes ? MPI-1: no MPI-2: yes

Edgar Gabriel MPI_Type_get_envelope MPI_Type_get_envelope ( MPI_Datatype datatype, int *num_integers, int *num_addresses, int *num_datatypes, int *combiner ); The combiner field returns how the datatype was created, e.g. –MPI_COMBINER_NAMED: basic datatype –MPI_COMBINER_CONTIGUOS: MPI_Type_contiguous –MPI_COMBINER_VECTOR: MPI_Type_vector –MPI_COMBINER_INDEXED: MPI_Type_indexed –MPI_COMBINER_STRUCT: MPI_Type_struct The other fields indicate how large the integer-array, the datatype-array, and the address-array has to be for the following call to MPI_Type_get_contents

Edgar Gabriel MPI_Type_get_contents MPI_Type_get_contents ( MPI_Datatype datatype, int max_integer, int max_addresses, int max_datatypes, int *integers, int *addresses, MPI_Datatype *dts); Call is erroneous for a predefined datatypes If returned data types are derived datatypes, then objects are duplicates of the original derived datatypes. User has to free them using MPI_Type_free The values in the integer, addresses and datatype arrays are depending on the original datatype constructor Type decoding functions available for MPICH or MPICH2 or LAM7.0.x

Edgar Gabriel Examples using MPI_Type_get_contents e.g. for MPI_Type_struct countintegers[0] blocklengths[]integers[1] – integers[integers[0]] displacements[]addresses[0]–addresses[integers[0]-1] datatypes[]dts[0] – dts[integers[0]-1] e.g. for MPI_Type_contiguous countintegers[0] datatypedts[0] For the complete list, see the MPI-2 specification

Edgar Gabriel The Info-object General mechanism in MPI-2 to pass hints to the MPI library Used in –Dynamic processes management –One-sided operations –Parallel File I/O An Info-object is a pair of ( key, value ) Key and value are both character strings Separate functions introduced by MPI, since many languages do not have good support for handling character strings

Edgar Gabriel The Info-object cont. Key and value are case-sensitive A key may just have one value attached to it If an implementation does not recognize a key, it will ignore it Maximum length for key: MPI_MAX_INFO_KEY Maximum length for value: MPI_MAX_INFO_VAL

Edgar Gabriel Handling Info-objects Create a new Info object MPI_Info_create ( MPI_Info *info ); Add a (key, value) pair –Overrides previous value, if key already known MPI_Info_set ( MPI_Info info, char *key, char *val); Delete a (key, value) pair MPI_Info_delete ( MPI_Info info, char *key); Determine a value for a certain key –Flag indicates, whether key was recognized MPI_Info_get ( MPI_Info info, char *key, int valuelen, char *val, int *flag); Destroy an Info object MPI_Info_free ( MPI_Info *info);